3ANL

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) complexed with pyridin-2-ylmethylphosphonic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EGH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62770.1M sodium citrate, 0.8M sodium malonate, 0.3M potassium sodium (+) tartrate, 3mM NADPH, 5mM MgCl2, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5752.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.717α = 90
b = 59.298β = 90
c = 87.166γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2102010-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.15099.53.556038557580.00010.0001
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1499.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2EGH2.129.25319952715282299.30.185760.183690.22518RANDOM22.825
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.590.58-1.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.025
r_dihedral_angle_4_deg20.848
r_dihedral_angle_3_deg15.691
r_dihedral_angle_1_deg5.588
r_scangle_it4.687
r_scbond_it3.016
r_mcangle_it1.842
r_angle_refined_deg1.804
r_mcbond_it1.128
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.025
r_dihedral_angle_4_deg20.848
r_dihedral_angle_3_deg15.691
r_dihedral_angle_1_deg5.588
r_scangle_it4.687
r_scbond_it3.016
r_mcangle_it1.842
r_angle_refined_deg1.804
r_mcbond_it1.128
r_nbtor_refined0.301
r_nbd_refined0.219
r_symmetry_vdw_refined0.213
r_xyhbond_nbd_refined0.161
r_chiral_restr0.141
r_symmetry_hbond_refined0.134
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6061
Nucleic Acid Atoms
Solvent Atoms413
Heterogen Atoms118

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling